2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2010 Christian M. Zmasek
8 // This library is free software; you can redistribute it and/or
9 // modify it under the terms of the GNU Lesser General Public
10 // License as published by the Free Software Foundation; either
11 // version 2.1 of the License, or (at your option) any later version.
13 // This library is distributed in the hope that it will be useful,
14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 // Lesser General Public License for more details.
18 // You should have received a copy of the GNU Lesser General Public
19 // License along with this library; if not, write to the Free Software
20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
22 // Contact: phylosoft @ gmail . com
23 // WWW: www.phylosoft.org/forester
25 package org.forester.archaeopteryx;
27 import java.awt.Component;
28 import java.awt.Container;
30 import java.awt.event.ActionEvent;
31 import java.awt.event.ActionListener;
32 import java.io.IOException;
33 import java.util.List;
34 import java.util.Locale;
37 import javax.swing.JApplet;
38 import javax.swing.JCheckBoxMenuItem;
39 import javax.swing.JFrame;
40 import javax.swing.JMenu;
41 import javax.swing.JMenuBar;
42 import javax.swing.JMenuItem;
43 import javax.swing.JOptionPane;
44 import javax.swing.JRadioButtonMenuItem;
46 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
47 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
48 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
49 import org.forester.phylogeny.Phylogeny;
50 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
51 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
52 import org.forester.util.ForesterConstants;
53 import org.forester.util.ForesterUtil;
55 public abstract class MainFrame extends JFrame implements ActionListener {
57 static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";
58 static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME
59 static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;
60 private static final long serialVersionUID = 3655000897845508358L;
61 final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),
64 static final String TYPE_MENU_HEADER = "Type";
65 static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";
66 static final String EURO_TYPE_CBMI_LABEL = "Euro Type";
67 static final String CURVED_TYPE_CBMI_LABEL = "Curved";
68 static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";
69 static final String CONVEX_TYPE_CBMI_LABEL = "Convex";
70 static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";
71 static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO
72 static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO
73 static final String OPTIONS_HEADER = "Options";
74 static final String SEARCH_SUBHEADER = "Search:";
75 static final String DISPLAY_SUBHEADER = "Display:";
76 static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";
77 static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";
78 static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
79 static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
80 static final String DISPLAY_SCALE_LABEL = "Display Scale";
81 static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";
82 static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";
83 static final String LABEL_DIRECTION_LABEL = "Radial Labels";
84 static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";
85 static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
86 static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
87 static final String BG_GRAD_LABEL = "Background Color Gradient";
88 static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Shapes";
89 static final String SHOW_OVERVIEW_LABEL = "Show Overview";
90 static final String FONT_SIZE_MENU_LABEL = "Font Size";
91 static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
92 static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
93 static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
94 static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
95 static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
96 static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";
97 static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";
98 static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";
103 JMenu _options_jmenu;
104 JMenu _font_size_menu;
106 JMenuItem[] _load_phylogeny_from_webservice_menu_items;
108 JMenuItem _open_item;
109 JMenuItem _open_url_item;
110 JMenuItem _save_item;
111 JMenuItem _save_all_item;
112 JMenuItem _close_item;
113 JMenuItem _exit_item;
116 JMenuItem _midpoint_root_item;
117 JMenuItem _taxcolor_item;
118 JMenuItem _confcolor_item;
119 JMenuItem _infer_common_sn_names_item;
120 JMenuItem _collapse_species_specific_subtrees;
121 JMenuItem _collapse_below_threshold; //TODO implememt me
122 JMenuItem _obtain_detailed_taxonomic_information_jmi;
123 JMenuItem _obtain_uniprot_seq_information_jmi;
124 JMenuItem _move_node_names_to_tax_sn_jmi;
125 JMenuItem _move_node_names_to_seq_names_jmi;
126 JMenuItem _extract_tax_code_from_node_names_jmi;
128 JMenuItem _super_tiny_fonts_item;
129 JMenuItem _tiny_fonts_item;
130 JMenuItem _small_fonts_item;
131 JMenuItem _medium_fonts_item;
132 JMenuItem _large_fonts_item;
134 // _ screen and print
135 JMenuItem _choose_font_mi;
136 JMenuItem _switch_colors_mi;
137 JCheckBoxMenuItem _label_direction_cbmi;
139 JCheckBoxMenuItem _screen_antialias_cbmi;
140 JCheckBoxMenuItem _background_gradient_cbmi;
141 JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;
142 JRadioButtonMenuItem _uniform_cladograms_rbmi;
143 JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;
144 JCheckBoxMenuItem _show_branch_length_values_cbmi;
145 JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
146 JCheckBoxMenuItem _show_overview_cbmi;
147 JCheckBoxMenuItem _show_domain_labels;
148 JCheckBoxMenuItem _abbreviate_scientific_names;
149 JCheckBoxMenuItem _color_labels_same_as_parent_branch;
150 JMenuItem _overview_placment_mi;
151 JMenuItem _choose_minimal_confidence_mi;
152 JCheckBoxMenuItem _show_default_node_shapes_cbmi;
153 JMenuItem _cycle_node_shape_mi;
154 JMenuItem _cycle_node_fill_mi;
155 JMenuItem _choose_node_size_mi;
156 JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
158 JCheckBoxMenuItem _graphics_export_visible_only_cbmi;
159 JCheckBoxMenuItem _antialias_print_cbmi;
160 JCheckBoxMenuItem _print_black_and_white_cbmi;
161 JCheckBoxMenuItem _print_using_actual_size_cbmi;
162 JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;
163 JMenuItem _print_size_mi;
164 JMenuItem _choose_pdf_width_mi;
166 JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
167 JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
168 JCheckBoxMenuItem _replace_underscores_cbmi;
170 JCheckBoxMenuItem _search_case_senstive_cbmi;
171 JCheckBoxMenuItem _search_whole_words_only_cbmi;
172 JCheckBoxMenuItem _inverse_search_result_cbmi;
175 JCheckBoxMenuItem _rectangular_type_cbmi;
176 JCheckBoxMenuItem _triangular_type_cbmi;
177 JCheckBoxMenuItem _curved_type_cbmi;
178 JCheckBoxMenuItem _convex_type_cbmi;
179 JCheckBoxMenuItem _euro_type_cbmi;
180 JCheckBoxMenuItem _rounded_type_cbmi;
181 JCheckBoxMenuItem _unrooted_type_cbmi;
182 JCheckBoxMenuItem _circular_type_cbmi;
183 // view as text menu:
184 JMenuItem _view_as_NH_item;
185 JMenuItem _view_as_NHX_item;
186 JMenuItem _view_as_XML_item;
187 JMenuItem _view_as_nexus_item;
188 JMenuItem _display_basic_information_item;
190 JMenuItem _about_item;
191 JMenuItem _help_item;
192 JMenuItem _website_item;
193 JMenuItem _phyloxml_website_item;
194 JMenuItem _phyloxml_ref_item;
195 JMenuItem _aptx_ref_item;
196 // Handy pointers to child components:
197 MainPanel _mainpanel;
198 Container _contentpane;
199 TextFrame _textframe;
200 Configuration _configuration;
201 JMenuItem _remove_branch_color_item;
205 // Empty constructor.
211 public void actionPerformed( final ActionEvent e ) {
212 final Object o = e.getSource();
213 boolean is_applet = false;
214 JApplet applet = null;
215 if ( getCurrentTreePanel() != null ) {
216 is_applet = getCurrentTreePanel().isApplet();
218 applet = getCurrentTreePanel().obtainApplet();
221 if ( o == _open_url_item ) {
222 readPhylogeniesFromURL();
224 else if ( o == _exit_item ) {
227 else if ( o == _taxcolor_item ) {
230 else if ( o == _confcolor_item ) {
233 else if ( o == _infer_common_sn_names_item ) {
234 if ( isSubtreeDisplayed() ) {
237 if ( getCurrentTreePanel() != null ) {
238 getCurrentTreePanel().inferCommonPartOfScientificNames();
241 else if ( o == _collapse_species_specific_subtrees ) {
242 if ( isSubtreeDisplayed() ) {
245 if ( getCurrentTreePanel() != null ) {
246 getCurrentTreePanel().collapseSpeciesSpecificSubtrees();
249 else if ( o == _remove_branch_color_item ) {
250 if ( isSubtreeDisplayed() ) {
253 removeBranchColors();
255 else if ( o == _midpoint_root_item ) {
256 if ( isSubtreeDisplayed() ) {
261 else if ( o == _switch_colors_mi ) {
264 else if ( o == _display_basic_information_item ) {
265 displayBasicInformation();
267 else if ( o == _view_as_NH_item ) {
270 else if ( o == _view_as_NHX_item ) {
273 else if ( o == _view_as_XML_item ) {
276 else if ( o == _view_as_nexus_item ) {
279 else if ( o == _super_tiny_fonts_item ) {
280 if ( getCurrentTreePanel() != null ) {
281 getCurrentTreePanel().setSuperTinyFonts();
282 getCurrentTreePanel().repaint();
285 else if ( o == _tiny_fonts_item ) {
286 if ( getCurrentTreePanel() != null ) {
287 getCurrentTreePanel().setTinyFonts();
288 getCurrentTreePanel().repaint();
291 else if ( o == _small_fonts_item ) {
292 if ( getCurrentTreePanel() != null ) {
293 getCurrentTreePanel().setSmallFonts();
294 getCurrentTreePanel().repaint();
297 else if ( o == _medium_fonts_item ) {
298 if ( getCurrentTreePanel() != null ) {
299 getCurrentTreePanel().setMediumFonts();
300 getCurrentTreePanel().repaint();
303 else if ( o == _large_fonts_item ) {
304 if ( getCurrentTreePanel() != null ) {
305 getCurrentTreePanel().setLargeFonts();
306 getCurrentTreePanel().repaint();
309 else if ( o == _choose_font_mi ) {
312 else if ( o == _choose_minimal_confidence_mi ) {
313 chooseMinimalConfidence();
315 else if ( o == _choose_node_size_mi ) {
316 chooseNodeSize( getOptions(), this );
318 else if ( o == _overview_placment_mi ) {
319 MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
321 else if ( o == _cycle_node_fill_mi ) {
322 MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
324 else if ( o == _cycle_node_shape_mi ) {
325 MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
327 else if ( o == _screen_antialias_cbmi ) {
328 updateOptions( getOptions() );
329 updateScreenTextAntialias( getMainPanel().getTreePanels() );
331 else if ( o == _background_gradient_cbmi ) {
332 updateOptions( getOptions() );
334 else if ( o == _show_domain_labels ) {
335 updateOptions( getOptions() );
337 else if ( o == _abbreviate_scientific_names ) {
338 updateOptions( getOptions() );
340 else if ( o == _color_labels_same_as_parent_branch ) {
341 updateOptions( getOptions() );
343 else if ( o == _show_default_node_shapes_cbmi ) {
344 updateOptions( getOptions() );
346 else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
347 updateOptions( getOptions() );
349 else if ( o == _non_lined_up_cladograms_rbmi ) {
350 updateOptions( getOptions() );
353 else if ( o == _uniform_cladograms_rbmi ) {
354 updateOptions( getOptions() );
357 else if ( o == _ext_node_dependent_cladogram_rbmi ) {
358 updateOptions( getOptions() );
361 else if ( o == _search_case_senstive_cbmi ) {
362 updateOptions( getOptions() );
363 getMainPanel().getControlPanel().search();
365 else if ( o == _search_whole_words_only_cbmi ) {
366 updateOptions( getOptions() );
367 getMainPanel().getControlPanel().search();
369 else if ( o == _inverse_search_result_cbmi ) {
370 updateOptions( getOptions() );
371 getMainPanel().getControlPanel().search();
373 else if ( o == _show_scale_cbmi ) {
374 updateOptions( getOptions() );
376 else if ( o == _show_branch_length_values_cbmi ) {
377 updateOptions( getOptions() );
379 else if ( o == _label_direction_cbmi ) {
380 updateOptions( getOptions() );
382 else if ( o == _show_overview_cbmi ) {
383 updateOptions( getOptions() );
384 if ( getCurrentTreePanel() != null ) {
385 getCurrentTreePanel().updateOvSizes();
388 else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
389 || ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
390 || ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
393 else if ( o == _about_item ) {
396 else if ( o == _help_item ) {
397 help( getConfiguration().getWebLinks() );
399 else if ( o == _website_item ) {
401 Util.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet );
403 catch ( final IOException e1 ) {
404 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
407 else if ( o == _phyloxml_website_item ) {
409 Util.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet );
411 catch ( final IOException e1 ) {
412 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
415 else if ( o == _aptx_ref_item ) {
417 Util.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet );
419 catch ( final IOException e1 ) {
420 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
423 else if ( o == _phyloxml_ref_item ) {
425 Util.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );
427 catch ( final IOException e1 ) {
428 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
432 if ( _load_phylogeny_from_webservice_menu_items != null ) {
433 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
434 if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {
435 readPhylogeniesFromWebservice( i );
440 _contentpane.repaint();
443 boolean isSubtreeDisplayed() {
444 if ( getCurrentTreePanel() != null ) {
445 if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
447 .showMessageDialog( this,
448 "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
449 "Operation can not be exectuted on a sub-tree",
450 JOptionPane.WARNING_MESSAGE );
457 void activateSaveAllIfNeeded() {
458 if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
459 _save_all_item.setEnabled( true );
462 _save_all_item.setEnabled( false );
466 void buildFileMenu() {
467 _file_jmenu = createMenu( "File", getConfiguration() );
468 _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
469 _file_jmenu.addSeparator();
470 _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
471 customizeJMenuItem( _open_url_item );
472 customizeJMenuItem( _exit_item );
473 _jmenubar.add( _file_jmenu );
476 void buildFontSizeMenu() {
477 _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
478 _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
479 _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
480 _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
481 _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
482 _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
483 customizeJMenuItem( _super_tiny_fonts_item );
484 customizeJMenuItem( _tiny_fonts_item );
485 customizeJMenuItem( _small_fonts_item );
486 customizeJMenuItem( _medium_fonts_item );
487 customizeJMenuItem( _large_fonts_item );
488 _jmenubar.add( _font_size_menu );
491 void buildHelpMenu() {
492 _help_jmenu = createMenu( "Help", getConfiguration() );
493 _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
494 _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
495 _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
496 _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
497 _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
498 _help_jmenu.addSeparator();
499 _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
500 customizeJMenuItem( _help_item );
501 customizeJMenuItem( _website_item );
502 customizeJMenuItem( _phyloxml_website_item );
503 customizeJMenuItem( _aptx_ref_item );
504 customizeJMenuItem( _phyloxml_ref_item );
505 customizeJMenuItem( _about_item );
506 _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );
507 _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );
508 _jmenubar.add( _help_jmenu );
511 void buildTypeMenu() {
512 _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
513 _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
514 _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );
515 _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );
516 _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );
517 _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );
518 _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );
519 _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );
520 _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );
521 customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );
522 customizeCheckBoxMenuItem( _triangular_type_cbmi, false );
523 customizeCheckBoxMenuItem( _euro_type_cbmi, false );
524 customizeCheckBoxMenuItem( _rounded_type_cbmi, false );
525 customizeCheckBoxMenuItem( _curved_type_cbmi, false );
526 customizeCheckBoxMenuItem( _convex_type_cbmi, false );
527 customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
528 customizeCheckBoxMenuItem( _circular_type_cbmi, false );
529 _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
530 _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
531 initializeTypeMenu( getOptions() );
532 _jmenubar.add( _type_menu );
535 void buildViewMenu() {
536 _view_jmenu = createMenu( "View", getConfiguration() );
537 _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
538 _view_jmenu.addSeparator();
539 _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
540 _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
541 _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
542 _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
543 customizeJMenuItem( _display_basic_information_item );
544 customizeJMenuItem( _view_as_NH_item );
545 customizeJMenuItem( _view_as_NHX_item );
546 customizeJMenuItem( _view_as_XML_item );
547 customizeJMenuItem( _view_as_nexus_item );
548 _jmenubar.add( _view_jmenu );
551 private void chooseFont() {
552 final FontChooser fc = new FontChooser();
553 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
554 fc.showDialog( this, "Select the Base Font" );
555 getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
558 private void chooseMinimalConfidence() {
559 final String s = ( String ) JOptionPane
560 .showInputDialog( this,
561 "Please enter the minimum for confidence values to be displayed.\n"
562 + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
563 "Minimal Confidence Value",
564 JOptionPane.QUESTION_MESSAGE,
567 getOptions().getMinConfidenceValue() );
568 if ( !ForesterUtil.isEmpty( s ) ) {
569 boolean success = true;
571 final String m_str = s.trim();
572 if ( !ForesterUtil.isEmpty( m_str ) ) {
574 m = Double.parseDouble( m_str );
576 catch ( final Exception ex ) {
583 if ( success && ( m >= 0.0 ) ) {
584 getOptions().setMinConfidenceValue( m );
589 static void chooseNodeSize( final Options options, final Component parent ) {
590 final String s = ( String ) JOptionPane.showInputDialog( parent,
591 "Please enter the default size for node shapes.\n"
593 + options.getDefaultNodeShapeSize() + "]\n",
595 JOptionPane.QUESTION_MESSAGE,
598 options.getDefaultNodeShapeSize() );
599 if ( !ForesterUtil.isEmpty( s ) ) {
600 boolean success = true;
602 final String m_str = s.trim();
603 if ( !ForesterUtil.isEmpty( m_str ) ) {
605 m = Double.parseDouble( m_str );
607 catch ( final Exception ex ) {
614 if ( success && ( m >= 0.0 ) ) {
615 final short size = ForesterUtil.roundToShort( m );
617 options.setDefaultNodeShapeSize( size );
625 if ( _mainpanel != null ) {
626 _mainpanel.terminate();
628 if ( _contentpane != null ) {
629 _contentpane.removeAll();
636 if ( _mainpanel.getCurrentTreePanel() != null ) {
637 _mainpanel.getCurrentTreePanel().confColor();
641 void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
642 if ( item != null ) {
643 item.setFont( MainFrame.menu_font );
644 if ( !getConfiguration().isUseNativeUI() ) {
645 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
646 item.setForeground( getConfiguration().getGuiMenuTextColor() );
648 item.setSelected( is_selected );
649 item.addActionListener( this );
653 void customizeJMenuItem( final JMenuItem jmi ) {
655 jmi.setFont( MainFrame.menu_font );
656 if ( !getConfiguration().isUseNativeUI() ) {
657 jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
658 jmi.setForeground( getConfiguration().getGuiMenuTextColor() );
660 jmi.addActionListener( this );
664 void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
665 if ( item != null ) {
666 item.setFont( MainFrame.menu_font );
667 if ( !getConfiguration().isUseNativeUI() ) {
668 item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
669 item.setForeground( getConfiguration().getGuiMenuTextColor() );
671 item.setSelected( is_selected );
672 item.addActionListener( this );
676 void exceptionOccuredDuringOpenFile( final Exception e ) {
678 _mainpanel.getCurrentTreePanel().setArrowCursor();
680 catch ( final Exception ex ) {
683 JOptionPane.showMessageDialog( this,
684 ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
685 "Error during File|Open",
686 JOptionPane.ERROR_MESSAGE );
689 void exceptionOccuredDuringSaveAs( final Exception e ) {
691 _mainpanel.getCurrentTreePanel().setArrowCursor();
693 catch ( final Exception ex ) {
696 JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
699 boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
700 if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
701 JOptionPane.showMessageDialog( this,
702 "Gene tree and species tree have no species in common.",
704 JOptionPane.ERROR_MESSAGE );
707 else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
708 JOptionPane.showMessageDialog( this,
709 "Gene tree and species tree have only one species in common.",
711 JOptionPane.ERROR_MESSAGE );
719 public Configuration getConfiguration() {
720 return _configuration;
723 TreePanel getCurrentTreePanel() {
724 return getMainPanel().getCurrentTreePanel();
727 JMenu getHelpMenu() {
731 JCheckBoxMenuItem getlabelDirectionCbmi() {
732 return _label_direction_cbmi;
735 MainPanel getMainPanel() {
739 JMenuBar getMenuBarOfMainFrame() {
743 Options getOptions() {
747 void initializeTypeMenu( final Options options ) {
748 setTypeMenuToAllUnselected();
749 switch ( options.getPhylogenyGraphicsType() ) {
751 _convex_type_cbmi.setSelected( true );
754 _curved_type_cbmi.setSelected( true );
757 _euro_type_cbmi.setSelected( true );
760 _rounded_type_cbmi.setSelected( true );
763 _triangular_type_cbmi.setSelected( true );
766 _unrooted_type_cbmi.setSelected( true );
769 _circular_type_cbmi.setSelected( true );
772 _rectangular_type_cbmi.setSelected( true );
777 void midpointRoot() {
778 if ( _mainpanel.getCurrentTreePanel() != null ) {
779 _mainpanel.getCurrentTreePanel().midpointRoot();
783 abstract void readPhylogeniesFromURL();
785 void readPhylogeniesFromWebservice( final int i ) {
786 final UrlTreeReader reader = new UrlTreeReader( this, i );
787 new Thread( reader ).start();
790 private void removeBranchColors() {
791 if ( getMainPanel().getCurrentPhylogeny() != null ) {
792 Util.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
796 void removeTextFrame() {
797 if ( _textframe != null ) {
803 void setConfiguration( final Configuration configuration ) {
804 _configuration = configuration;
807 void setOptions( final Options options ) {
811 void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
812 setTypeMenuToAllUnselected();
815 _circular_type_cbmi.setSelected( true );
818 _convex_type_cbmi.setSelected( true );
821 _curved_type_cbmi.setSelected( true );
824 _euro_type_cbmi.setSelected( true );
827 _rounded_type_cbmi.setSelected( true );
830 _rectangular_type_cbmi.setSelected( true );
833 _triangular_type_cbmi.setSelected( true );
836 _unrooted_type_cbmi.setSelected( true );
839 throw new IllegalArgumentException( "unknown type: " + type );
843 void setTypeMenuToAllUnselected() {
844 _convex_type_cbmi.setSelected( false );
845 _curved_type_cbmi.setSelected( false );
846 _euro_type_cbmi.setSelected( false );
847 _rounded_type_cbmi.setSelected( false );
848 _triangular_type_cbmi.setSelected( false );
849 _rectangular_type_cbmi.setSelected( false );
850 _unrooted_type_cbmi.setSelected( false );
851 _circular_type_cbmi.setSelected( false );
854 public void showWhole() {
855 _mainpanel.getControlPanel().showWhole();
858 void switchColors() {
859 final TreeColorSet colorset = _mainpanel.getTreeColorSet();
860 final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
861 csc.setVisible( true );
865 if ( _mainpanel.getCurrentTreePanel() != null ) {
866 _mainpanel.getCurrentTreePanel().taxColor();
870 void typeChanged( final Object o ) {
871 updateTypeCheckboxes( getOptions(), o );
872 updateOptions( getOptions() );
873 if ( getCurrentTreePanel() != null ) {
874 final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();
875 final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();
876 if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
877 || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )
878 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )
879 || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {
880 getCurrentTreePanel().getControlPanel().showWhole();
882 if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
883 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );
886 getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );
888 getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );
889 updateScreenTextAntialias( getMainPanel().getTreePanels() );
890 if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {
891 if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
892 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );
895 getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );
901 void updateOptions( final Options options ) {
902 options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
903 options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
904 && _background_gradient_cbmi.isSelected() );
905 options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
906 options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
907 && _abbreviate_scientific_names.isSelected() );
908 options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
909 && _color_labels_same_as_parent_branch.isSelected() );
910 options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
911 && _show_default_node_shapes_cbmi.isSelected() );
912 options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
913 && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
914 if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
915 options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
917 else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
918 options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
920 else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
921 options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
923 options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
924 && _search_case_senstive_cbmi.isSelected() );
925 if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
926 options.setShowScale( _show_scale_cbmi.isSelected() );
928 if ( _label_direction_cbmi != null ) {
929 if ( _label_direction_cbmi.isSelected() ) {
930 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
933 options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
936 options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
937 if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
938 options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
940 options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )
941 && ( _print_using_actual_size_cbmi.isSelected() ) );
942 options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
943 && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
944 options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
945 options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )
946 && _print_black_and_white_cbmi.isSelected() );
947 options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
948 && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
949 options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
950 && _extract_pfam_style_tax_codes_cbmi.isSelected() );
951 options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
952 && _replace_underscores_cbmi.isSelected() );
953 options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
954 && _search_whole_words_only_cbmi.isSelected() );
955 options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
956 && _inverse_search_result_cbmi.isSelected() );
957 if ( _graphics_export_visible_only_cbmi != null ) {
958 options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
959 if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
960 _graphics_export_using_actual_size_cbmi.setSelected( true );
961 _graphics_export_using_actual_size_cbmi.setEnabled( false );
964 _graphics_export_using_actual_size_cbmi.setEnabled( true );
967 if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
968 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
970 else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {
971 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
973 else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {
974 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
976 else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {
977 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
979 else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {
980 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
982 else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {
983 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
985 else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {
986 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
988 else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
989 options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
993 void updateTypeCheckboxes( final Options options, final Object o ) {
994 setTypeMenuToAllUnselected();
995 ( ( JCheckBoxMenuItem ) o ).setSelected( true );
998 void displayBasicInformation() {
999 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
1002 _textframe = TextFrame.instantiate( Util.crateBasicInformation( _mainpanel.getCurrentPhylogeny() ) );
1005 void viewAsNexus() {
1007 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1008 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1011 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNexus() );
1016 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1017 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1020 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshire( false ) );
1025 if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty()
1026 || ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() > 10000 ) ) {
1029 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toNewHampshireX() );
1034 if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty()
1035 && ( _mainpanel.getCurrentPhylogeny().getNumberOfExternalNodes() <= 10000 ) ) {
1036 _textframe = TextFrame.instantiate( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ) );
1041 * Display the about box.
1043 static void about() {
1044 final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
1045 about.append( "Copyright (C) 2007-2011 Christian Zmasek\n" );
1046 about.append( "All Rights Reserved\n" );
1047 about.append( "License: GNU Lesser General Public License (LGPL)\n" );
1048 about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
1049 about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1050 about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
1051 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1052 about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );
1054 if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )
1055 && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {
1056 about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "
1057 + ForesterUtil.OS_VERSION + "]\n" );
1059 final Runtime rt = java.lang.Runtime.getRuntime();
1060 final long free_memory = rt.freeMemory() / 1000000;
1061 final long total_memory = rt.totalMemory() / 1000000;
1062 about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );
1063 about.append( "[locale: " + Locale.getDefault() + "]\n" );
1064 about.append( "References:\n" );
1065 about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );
1066 about.append( "For more information & download:\n" );
1067 about.append( Constants.APTX_WEB_SITE + "\n" );
1068 about.append( "Comments: " + Constants.AUTHOR_EMAIL );
1069 JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
1072 static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
1073 return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
1076 static JMenu createMenu( final String title, final Configuration conf ) {
1077 final JMenu jmenu = new JMenu( title );
1078 if ( !conf.isUseNativeUI() ) {
1079 jmenu.setFont( MainFrame.menu_font );
1080 jmenu.setBackground( conf.getGuiMenuBackgroundColor() );
1081 jmenu.setForeground( conf.getGuiMenuTextColor() );
1086 static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {
1087 label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );
1088 if ( !configuration.isUseNativeUI() ) {
1089 label.setBackground( configuration.getGuiMenuBackgroundColor() );
1090 label.setForeground( configuration.getGuiMenuTextColor() );
1091 label.setOpaque( true );
1093 label.setSelected( false );
1094 label.setEnabled( false );
1098 static void cycleOverview( final Options op, final TreePanel tree_panel ) {
1099 switch ( op.getOvPlacement() ) {
1101 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
1104 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
1107 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
1110 op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
1113 throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
1115 if ( tree_panel != null ) {
1116 tree_panel.updateOvSettings();
1120 static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
1121 switch ( op.getDefaultNodeFill() ) {
1123 op.setDefaultNodeFill( NodeFill.SOLID );
1126 op.setDefaultNodeFill( NodeFill.GRADIENT );
1129 op.setDefaultNodeFill( NodeFill.NONE );
1132 throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );
1136 static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {
1137 switch ( op.getDefaultNodeShape() ) {
1139 op.setDefaultNodeShape( NodeShape.RECTANGLE );
1142 op.setDefaultNodeShape( NodeShape.CIRCLE );
1145 throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );
1149 static void help( final Map<String, WebLink> weblinks ) {
1150 final StringBuilder sb = new StringBuilder();
1151 sb.append( "Display options\n" );
1152 sb.append( "-------------------\n" );
1153 sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
1154 sb.append( "Clickable tree nodes\n" );
1155 sb.append( "--------------------\n" );
1156 sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
1157 sb.append( "or by right clicking:\n" );
1158 sb.append( "o Display Node Data -- display information for a node\n" );
1159 sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
1160 sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
1161 sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
1162 sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
1163 sb.append( "o Colorize Subtree -- color a subtree\n" );
1164 sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
1165 sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
1166 sb.append( "- there may be additional choices depending on this particular setup\n\n" );
1167 sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
1168 sb.append( "Zooming\n" );
1169 sb.append( "---------\n" );
1170 sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
1171 sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
1172 sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
1173 sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
1174 sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
1175 sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
1176 sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
1177 sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
1178 sb.append( "Quick tree manipulation:\n" );
1179 sb.append( "------------------------\n" );
1180 sb.append( "Order Subtrees -- order the tree by branch length\n" );
1181 sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
1182 sb.append( "Memory problems (Java heap space error)\n" );
1183 sb.append( "---------------------------------------\n" );
1184 sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
1185 sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
1186 sb.append( "the '-Xmx' Java command line option. For example:\n" );
1187 sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
1188 if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
1189 sb.append( "Active web links\n" );
1190 sb.append( "--------------------\n" );
1191 for( final String key : weblinks.keySet() ) {
1192 sb.append( " " + weblinks.get( key ).toString() + "\n" );
1195 // + "General remarks\n"
1196 // + "---------------\n"
1198 // "o The application version permits copying to the clipboard \n"
1200 // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
1202 // "o Changes made to a subtree affect this subtree and its subtrees,\n"
1203 // + " but not any of its parent tree(s).\n"
1205 // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
1207 // " are likely to be bootstrap values instead of branch length values.\n\n"
1209 // " Remarks regarding SDI (Speciation Duplication Inference):\n"
1211 // "o Each external node of the gene tree (in display) needs to be associated with\n"
1213 // " a species: either directly through the \"Species\" field, or the species\n"
1215 // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
1217 // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
1219 // "o A species tree for each species of the gene tree needs to be loaded with\n"
1221 // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
1223 // "o !External nodes of the gene tree associated with species not present in\n"
1225 // " the species tree are REMOVED prior to SDI execution!\n"
1227 // "o Both the gene tree and the species tree must be completely binary.\n"
1229 // "o Duplications and speciations are a function of the position of the root.\n"
1231 // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
1232 // + " incorrect and need to be inferred again\n"
1234 // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
1236 sb.append( "phyloXML\n" );
1237 sb.append( "-------------------\n" );
1238 sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
1239 sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
1240 sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
1242 sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
1243 sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
1244 TextFrame.instantiate( sb.toString() );
1247 static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
1248 if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
1249 mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
1252 mi.setText( "Cycle Overview Placement..." );
1256 static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {
1257 if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {
1258 mi.setText( "Cycle Node Shape Fill Type... (current: "
1259 + options.getDefaultNodeFill().toString().toLowerCase() + ")" );
1262 mi.setText( "Cycle Node Shape Fill Type..." );
1266 static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {
1267 if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {
1268 mi.setText( "Cycle Node Shape Fill Type... (current: "
1269 + options.getDefaultNodeShape().toString().toLowerCase() + ")" );
1272 mi.setText( "Cycle Node Shape Fill Type..." );
1276 static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
1277 if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
1278 mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
1281 mi.setText( "Select Colors..." );
1285 static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
1286 mi.setText( "Select Font... (current: " + font_desc + ")" );
1289 static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {
1290 if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {
1291 mi.setEnabled( true );
1293 else if ( ForesterUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {
1294 mi.setEnabled( true );
1297 mi.setEnabled( false );
1299 mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );
1302 static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {
1303 mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
1306 static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
1307 final JCheckBoxMenuItem scale,
1308 final JCheckBoxMenuItem branch_lengths,
1309 final JRadioButtonMenuItem non_lined_up,
1310 final JRadioButtonMenuItem uniform_clado,
1311 final JRadioButtonMenuItem nonuniform_clado,
1312 final JCheckBoxMenuItem label_direction_cbmi ) {
1313 final TreePanel tree_panel = main_panel.getCurrentTreePanel();
1314 final ControlPanel control = main_panel.getControlPanel();
1315 final Options options = main_panel.getOptions();
1316 scale.setSelected( options.isShowScale() );
1317 branch_lengths.setSelected( options.isShowBranchLengthValues() );
1318 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1319 if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
1320 scale.setSelected( false );
1321 scale.setEnabled( false );
1322 branch_lengths.setSelected( false );
1323 branch_lengths.setEnabled( false );
1325 else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
1326 scale.setSelected( false );
1327 scale.setEnabled( false );
1328 branch_lengths.setEnabled( true );
1331 scale.setEnabled( true );
1332 branch_lengths.setEnabled( true );
1334 if ( ( tree_panel != null )
1335 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
1336 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1337 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1338 branch_lengths.setSelected( false );
1339 branch_lengths.setEnabled( false );
1341 if ( tree_panel != null ) {
1342 if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
1343 || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
1344 non_lined_up.setEnabled( false );
1345 uniform_clado.setEnabled( false );
1346 nonuniform_clado.setEnabled( false );
1349 non_lined_up.setEnabled( true );
1350 uniform_clado.setEnabled( true );
1351 nonuniform_clado.setEnabled( true );
1355 if ( ( tree_panel != null )
1356 && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
1357 .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
1358 branch_lengths.setSelected( false );
1359 branch_lengths.setEnabled( false );
1361 if ( ( tree_panel != null )
1362 && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
1363 .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
1364 non_lined_up.setEnabled( false );
1367 // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
1368 non_lined_up.setEnabled( true );
1371 label_direction_cbmi.setEnabled( true );
1372 if ( tree_panel != null ) {
1373 if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1374 && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1375 label_direction_cbmi.setEnabled( false );
1377 if ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
1378 scale.setSelected( false );
1379 scale.setEnabled( false );
1384 static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
1385 for( final TreePanel tree_panel : treepanels ) {
1386 tree_panel.setTextAntialias();